plotDBN

This function can be used for plotting initial and transition structures of a dynamic Bayesian network.

Implementation of a collection of MCMC methods for Bayesian structure learning
of directed acyclic graphs (DAGs), both from continuous and discrete data. For efficient
inference on larger DAGs, the space of DAGs is pruned according to the data. To filter
the search space, the algorithm employs a hybrid approach, combining constraint-based
learning with search and score. A reduced search space is initially defined on the basis
of a skeleton obtained by means of the PC-algorithm, and then iteratively improved with
search and score. Search and score is then performed following two approaches:
Order MCMC, or Partition MCMC.
The BGe score is implemented for continuous data and the BDe score is implemented
for binary data or categorical data. The algorithms may provide the maximum a posteriori
(MAP) graph or a sample (a collection of DAGs) from the posterior distribution given the data.
All algorithms are also applicable for structure learning and sampling for dynamic Bayesian networks.
References:
J. Kuipers, P. Suter, G. Moffa (2022) <doi:10.1080/10618600.2021.2020127>,
N. Friedman and D. Koller (2003) <doi:10.1023/A:1020249912095>,
J. Kuipers and G. Moffa (2017) <doi:10.1080/01621459.2015.1133426>,
M. Kalisch et al. (2012) <doi:10.18637/jss.v047.i11>,
D. Geiger and D. Heckerman (2002) <doi:10.1214/aos/1035844981>,
P. Suter, J. Kuipers, G. Moffa, N.Beerenwinkel (2023) <doi:10.18637/jss.v105.i09>.

Polina Suter

BiDAG

Bayesian Inference for Directed Acyclic Graphs

plotDBN function

<dl><dt>DBN</dt>
<dd>binary matrix (or a graph object) representing a 2-step DBN (compact or unrolled)</dd>
<dt>struct</dt>
<dd>option used to determine if the initial or the transition structure should be plotted; acceptable values are init or trans</dd>
<dt>b</dt>
<dd>number of static variables in the DBN, 0 by default; note that for function to work correctly all static variables have to be in the first b columns of the matrix</dd>
<dt>shape</dt>
<dd>string, defining the shape of the box around each node; possible values are circle, ellipse, box</dd>
<dt>...</dt>
<dd>optional parameters passed to <code>Rgraphviz</code> plotting functions e.g. <code>main</code>, <code>fontsize</code></dd></dl>

Arguments

Author

Plotting a DBN — plotDBN

<dl>

<dt>DBN</dt>
<dd>binary matrix (or a graph object) representing a 2-step DBN (compact or unrolled)</dd>


<dt>struct</dt>
<dd>option used to determine if the initial or the transition structure should be plotted; acceptable values are init or trans</dd>


<dt>b</dt>
<dd>number of static variables in the DBN, 0 by default; note that for function to work correctly all static variables have to be in the first b columns of the matrix</dd>


<dt>shape</dt>
<dd>string, defining the shape of the box around each node; possible values are circle, ellipse, box</dd>


<dt>...</dt>
<dd>optional parameters passed to <code>Rgraphviz</code> plotting functions e.g. <code>main</code>, <code>fontsize</code></dd>

</dl>

plotDBN: Plotting a DBN

Description

Usage

Value

Arguments

Author

Examples